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学者姓名：朱晓玥
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Abstract ：
Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3-MYB TFs, we show that homodimerization can also directly change the recognized DNA motifs to distinguish between similar TFs. By high-throughput SELEX, we profiled the specificity landscape for 40 R2R3-MYBs of subfamily VIII and curated 833 motif models. The dimeric models show that homodimeric binding has evoked specificity changes for AtMYBs. Focusing on AtMYB2 as an example, we show that homodimerization has modified its specificity and allowed it to recognize additional cis-regulatory sequences that are different from the closely related CCWAA-box AtMYBs and are unique among all AtMYBs. Genomic sites described by the modified dimeric specificities of AtMYB2 are conserved in evolution and involved in AtMYB2-specific transcriptional activation. Collectively, this study provides rich data on sequence preferences of VIII R2R3-MYBs and suggests an alternative mechanism that guides closely related TFs to respective cis-regulatory sites.
Keyword ：
cis-elements cis-elements DNA binding specificity DNA binding specificity homodimerization homodimerization MYB family transcription factors MYB family transcription factors paralogs paralogs regulatory noncoding genome regulatory noncoding genome transcriptional regulation transcriptional regulation
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| GB/T 7714 | Li, Tian , Chen, Hao , Ma, Nana et al. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding [J]. | IMETA , 2025 , 4 (2) . |
| MLA | Li, Tian et al. "Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding" . | IMETA 4 . 2 (2025) . |
| APA | Li, Tian , Chen, Hao , Ma, Nana , Jiang, Dingkun , Wu, Jiacheng , Zhang, Xinfeng et al. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding . | IMETA , 2025 , 4 (2) . |
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Cannabis sativa L. has attracted increasing attention for its potential therapeutic applications, including anti- proliferative properties. In this study, we investigated the bioactivity of female flower extracts from eight cannabis varieties. The results showed significant variation in antiproliferative efficacy against three cancer cell lines (AGS, HCT116, and A549), antioxidant capacity, and total phenolic content. Two varieties, 'Galaxy CBD' and 'Mexican Sativa', were selected for widely targeted metabolomics analysis due to their contrasting anti- proliferative activity. Metabolomic analysis revealed distinct compositions of non-volatile and volatile metabolites between the two varieties, with 'Galaxy CBD' showing heightened levels of specific compounds associated with antiproliferative activity. Transcriptome analysis uncovered differential gene expression patterns across five stages of flower development, highlighting the genetic underpinnings of metabolic diversity. Integrating transcriptomic and metabolomic data revealed 'Galaxy CBD' exhibited higher expression of genes in pathways related to cannabinoid, terpenoid, and flavonoid biosynthesis, which may explain its superior antiproliferative activity. These findings provide valuable insights into the relationship between cannabis metabolite profiles, gene expression patterns and their potential medicinal properties, shedding light on the complex mechanisms underlying the antiproliferative properties of cannabis flower extracts.
Keyword ：
Antiproliferative activity Antiproliferative activity Cannabis sativa Cannabis sativa Medicinal properties Medicinal properties Metabolomics Metabolomics Transcriptomics Transcriptomics
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| GB/T 7714 | Liu, Ying , Li, Shuai , Shen, Mingwei et al. Integration of transcriptome and metabolome provides insights into metabolites and pathways associated with antiproliferative activity of cannabis flower extracts [J]. | INDUSTRIAL CROPS AND PRODUCTS , 2025 , 223 . |
| MLA | Liu, Ying et al. "Integration of transcriptome and metabolome provides insights into metabolites and pathways associated with antiproliferative activity of cannabis flower extracts" . | INDUSTRIAL CROPS AND PRODUCTS 223 (2025) . |
| APA | Liu, Ying , Li, Shuai , Shen, Mingwei , Guo, Foqin , Li, Minxuan , Cai, Sen et al. Integration of transcriptome and metabolome provides insights into metabolites and pathways associated with antiproliferative activity of cannabis flower extracts . | INDUSTRIAL CROPS AND PRODUCTS , 2025 , 223 . |
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Targeted insertion of large DNA sequences into plant genomes remains a major challenge in synthetic biology. Here, we evaluate the large serine recombinase Kp03 for site-specific integration of DNA fragments in rice and Arabidopsis. In transient protoplast assays, Kp03 mediates efficient insertion of donor DNA up to 27.3 kilobases (kb), with plasmid integration efficiencies reaching 99.1% for fragments up to 3.4 kb. Truncation experiments reveal that a minimal 15-bp attB sequence is necessary for integration. As a proof of concept, Kp03 successfully incorporates a 3.4-kb donor DNA into the rice genome at a locus containing this minimal attB sequence. Moreover, in rice callus, combining Kp03 with the NM-PE genome editing system to install a 26-bp attB site enables targeted integration of a 3.4-kb donor at the desired genomic locus. These findings establish Kp03 as a versatile tool for plant genome engineering, with broad applications for synthetic biology.
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| GB/T 7714 | Yan, Daqi , Meng, Yanyan , Zhang, Nan et al. Efficient site-specific integration of kilobase-length DNA fragments in plant cells via Kp03 recombinase [J]. | CELL REPORTS , 2025 , 44 (11) . |
| MLA | Yan, Daqi et al. "Efficient site-specific integration of kilobase-length DNA fragments in plant cells via Kp03 recombinase" . | CELL REPORTS 44 . 11 (2025) . |
| APA | Yan, Daqi , Meng, Yanyan , Zhang, Nan , Zhao, Yali , Ning, Conghui , Zhu, Lina et al. Efficient site-specific integration of kilobase-length DNA fragments in plant cells via Kp03 recombinase . | CELL REPORTS , 2025 , 44 (11) . |
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In a chamber-based digital PCR (dPCR) chip fabricated with polydimethylsiloxane (PDMS), bubble generation in the chambers at high temperatures is a critical issue. Here, we found that the main reason for bubble formation in PDMS chips is the too-high saturated vapor pressure of water at an elevated temperature. The bubbles should be completely prevented by reducing the initial pressure of the system to under 13.6 kPa to eliminate the effects of increased-pressure water vapor. Then, a cavity was designed and fabricated above the PCR reaction layer, and Parylene C was used as a shell covering the chip. The cavity was used for the negative generator in sample loading, PDMS degassing, PCR solution degassing in the digitization process and water storage in the thermal reaction process. The analysis was confirmed and finally achieved a desirable bubble-free, fast-digitization, valve-free and no-tubing connection dPCR.
Keyword ：
bubble generation bubble generation digital PCR chip digital PCR chip multifunction cavity multifunction cavity negative pressure environment negative pressure environment parylene C shell parylene C shell polydimethylsiloxane polydimethylsiloxane saturated vapor pressure of water saturated vapor pressure of water water loss water loss
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| GB/T 7714 | Gao, Shiyuan , Xu, Tiegang , Wu, Lei et al. Complete Prevention of Bubbles in a PDMS-Based Digital PCR Chip with a Multifunction Cavity [J]. | BIOSENSORS-BASEL , 2024 , 14 (3) . |
| MLA | Gao, Shiyuan et al. "Complete Prevention of Bubbles in a PDMS-Based Digital PCR Chip with a Multifunction Cavity" . | BIOSENSORS-BASEL 14 . 3 (2024) . |
| APA | Gao, Shiyuan , Xu, Tiegang , Wu, Lei , Zhu, Xiaoyue , Wang, Xuefeng , Chen, Ying et al. Complete Prevention of Bubbles in a PDMS-Based Digital PCR Chip with a Multifunction Cavity . | BIOSENSORS-BASEL , 2024 , 14 (3) . |
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We designed and fabricated a three-dimensional (3D) digital PCR (dPCR) chip for better sample compartmentalization and stronger fluorescent signals. The chip was made of glass, silicon and poly dimethylsiloxane (PDMS) layers, respectively. All the microstructures were fabricated on the silicon substrate, with high-density hexagonal-shape reaction units regularly arranged in the reaction zone. A common fed channel was located underneath the reaction units to maximize the use of the chip area. The reaction units and the flow channel were connected by cylindrical micro-holes, which made the oil-water two-phase system more stable and reduced the interference of fluorescence signals due to residual sample in the flow channel. In addition, fluorescent light reflection on the silicon surface enhanced the resolution of dPCR image.
Keyword ：
Digital PCR Digital PCR fluorescent light reflection fluorescent light reflection high-density high-density silicon silicon three-dimensional three-dimensional
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| GB/T 7714 | Gao, Shiyuan , Xu, Tiegang , Wu, Lei et al. A DIGITAL PCR CHIP WITH 3D STRUCTURE AND COMPOSITE MATERIALS [J]. | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS , 2024 : 665-668 . |
| MLA | Gao, Shiyuan et al. "A DIGITAL PCR CHIP WITH 3D STRUCTURE AND COMPOSITE MATERIALS" . | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS (2024) : 665-668 . |
| APA | Gao, Shiyuan , Xu, Tiegang , Wu, Lei , Zhu, Xiaoyue , Ma, Zhan , Li, Xinxin . A DIGITAL PCR CHIP WITH 3D STRUCTURE AND COMPOSITE MATERIALS . | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS , 2024 , 665-668 . |
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Aging is an irreversible pathophysiological process for all organisms. The accumulation of senescent cells in pathological sites or tissues is recognized as the major cause of diseases and disorders during the aging process. Small molecules that reduce senescent cell burdens have gained increasing attention as promising intervention therapeutics against aging, but effective anti-senescence agents remain rare. Camellia Sect. Chrysantha Chang is documented as a traditional Chinese herbal medicine used by ethnic groups for many medical and health benefits, but its effect on aging is unclear. Here, we investigated the anti-senescence potential of eight C. Sect. Chrysantha Chang species. The results show that ethyl acetate fractions from these C. Sect. Chrysantha Chang species were able to delay the senescence of H9c2 cardiomyocytes except for C. pingguoensis (CPg). N-butanol fractions of C. multipetala (CM), C. petelotii var. grandiflora (CPt), and C. longzhouensis (CL) showed a senescent cell clearance effect by altering the expression levels of senescent-associated marker genes in the DNA-damage response (DDR) pathway and the senescent cell anti-apoptotic pathway (SCAPs). By using UPLC-QTOF-MS-based non-targeted metabolomics analyses, 27 metabolites from Sect. Chrysantha species were putatively identified. Among them, high levels of sanchakasaponin C and D in CM, CPt, and CL were recognized as the key bioactive compounds responsible for senescent cell clearance. This study is the first to disclose and compare the anti-cell-senescence effect of a group of C. Sect. Chrysantha Chang, including some rare species. The combination of senescent markers and metabolomics analyses helped us to reveal the differences in chemical constituents that target senescent cells. Significantly, contrary to the C. chrysantha var. longistyla (CCL), which is widely cultivated and commercialized for tea drinks, CM, CPt, and CL contain unique chemicals for managing aging and aging-related diseases. The results from this study provide a foundation for species selection in developing small-molecule-based drugs to alleviate diseases and age-related dysfunctions and may potentially be useful for advancing geroscience research.
Keyword ：
anti-aging natural compounds anti-aging natural compounds Camellia Sect. Chrysantha Chang Camellia Sect. Chrysantha Chang cell senescence cell senescence metabolites metabolites
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| GB/T 7714 | Wu, Jiacheng , Bai, Quanzi , Chen, Jianghua et al. Systemic Analyses of Anti-Cell-Senescence Active Compounds in Camellia Sect. Chrysantha Chang and Their Mechanisms [J]. | PLANTS-BASEL , 2024 , 13 (15) . |
| MLA | Wu, Jiacheng et al. "Systemic Analyses of Anti-Cell-Senescence Active Compounds in Camellia Sect. Chrysantha Chang and Their Mechanisms" . | PLANTS-BASEL 13 . 15 (2024) . |
| APA | Wu, Jiacheng , Bai, Quanzi , Chen, Jianghua , Yang, Zhenbiao , Zhu, Xiaoyue . Systemic Analyses of Anti-Cell-Senescence Active Compounds in Camellia Sect. Chrysantha Chang and Their Mechanisms . | PLANTS-BASEL , 2024 , 13 (15) . |
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A one-step molding technique was developed to fabricate a PDMS chip containing both microstructures and macrostructures such as inlets, outlets and reservoirs. The most critical step for molding was to establish the connection between macroscale and microscale features, which was achieved by blocking the through hole of a rigid mold with an elastic cone. The elastic cones and macrostructures were fabricated on the elastic mold, while micro structures were fabricated on the rigid mold. As a result, a digital PCR chip with four sample throughputs has been successfully fabricated. This technique is expected to be used to fabricate a wide variety of microfluidic chips.
Keyword ：
one-step molding technique one-step molding technique PDMS chip PDMS chip reservoirs reservoirs soft lithography soft lithography
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| GB/T 7714 | Gao, Shiyuan , Xu, Tiegang , Wu, Lei et al. A ONE-STEP SOFT LITHOGRAPHY TECHNIQUE FOR MAKING MICROFLUIDIC PDMS CHIPS WITH MACRO-SCALE STRUCTURES [J]. | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS , 2024 : 1170-1173 . |
| MLA | Gao, Shiyuan et al. "A ONE-STEP SOFT LITHOGRAPHY TECHNIQUE FOR MAKING MICROFLUIDIC PDMS CHIPS WITH MACRO-SCALE STRUCTURES" . | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS (2024) : 1170-1173 . |
| APA | Gao, Shiyuan , Xu, Tiegang , Wu, Lei , Zhu, Xiaoyue , Li, Chunyong , Li, Xinxin . A ONE-STEP SOFT LITHOGRAPHY TECHNIQUE FOR MAKING MICROFLUIDIC PDMS CHIPS WITH MACRO-SCALE STRUCTURES . | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS , 2024 , 1170-1173 . |
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In this study, a high-pressure liquid environment thin-PDMS-film digital PCR (dPCR) system was developed. This platform features high quality, large surface area, low cost, fast thermal conduction speed, and easy operation, with a film thickness of 400 mu m and dimensions of 100 mm. 90 mm. Samples could be digitally processed within 100 s. And accurate and fast temperature shifts were achieved in designated reaction unit array area by a Peltier unit. Moreover, a heat-insulation lid with downwardly pointed edge was designed to efficiently prevent heat conduction around the chip. As a result, the total time could be achieved in less than 15 minutes for a forty-cycle PCR reaction.
Keyword ：
Digital PCR Digital PCR high-pressure liquid environment high-pressure liquid environment Peltier unit Peltier unit thin-PDMS-film thin-PDMS-film
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| GB/T 7714 | Gao, Shiyuan , Xu, Tiegang , Wu, Lei et al. HIGH-PRESSURE LIQUID ENVIRONMENT THIN-PDMS-FILM DIGITAL PCR [J]. | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS , 2024 : 1154-1157 . |
| MLA | Gao, Shiyuan et al. "HIGH-PRESSURE LIQUID ENVIRONMENT THIN-PDMS-FILM DIGITAL PCR" . | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS (2024) : 1154-1157 . |
| APA | Gao, Shiyuan , Xu, Tiegang , Wu, Lei , Zhu, Xiaoyue , Jiang, Lihong , Wang, Quan et al. HIGH-PRESSURE LIQUID ENVIRONMENT THIN-PDMS-FILM DIGITAL PCR . | 2024 IEEE 37TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, MEMS , 2024 , 1154-1157 . |
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The thermal expansion of gas and the air permeability of polydimethylsiloxane (PDMS) were previously thought to be the main causes of bubbles and water loss during polymerase chain reaction (PCR), resulting in a very complex chip design and operation. Here, by calculating and characterizing bubble formation, we discovered that water vapor is the main cause of bubbling. During PCR, heat increases the volume of the bubble by a factor of only similar to 0.2 in the absence of water vapor but by a factor of similar to 6.4 in the presence of water vapor. In addition, the phenomenon of "respiration" due to the repeated evaporation and condensation of water vapor accelerates the expansion of bubbles and the loss of water. A water seal above 109 kPa can effectively prevent bubbles in a bare PDMS chip with a simple structure, which is significant for the wide application of PDMS chips.
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| GB/T 7714 | Gao, Shiyuan , Xu, Tiegang , Wu, Lei et al. Overcoming bubble formation in polydimethylsiloxane-made PCR chips: mechanism and elimination with a high-pressure liquid seal [J]. | MICROSYSTEMS & NANOENGINEERING , 2024 , 10 (1) . |
| MLA | Gao, Shiyuan et al. "Overcoming bubble formation in polydimethylsiloxane-made PCR chips: mechanism and elimination with a high-pressure liquid seal" . | MICROSYSTEMS & NANOENGINEERING 10 . 1 (2024) . |
| APA | Gao, Shiyuan , Xu, Tiegang , Wu, Lei , Zhu, Xiaoyue , Wang, Xuefeng , Jian, Xiaohong et al. Overcoming bubble formation in polydimethylsiloxane-made PCR chips: mechanism and elimination with a high-pressure liquid seal . | MICROSYSTEMS & NANOENGINEERING , 2024 , 10 (1) . |
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Accurate sensing and responding to physical microenvironment are crucial for cell function and survival, but the underlying molecular mechanisms remain elusive. Pollen tube (PT) provides a perfect single -cell model for studying mechanobiology since it's naturally subjected to complex mechanical instructions from the pistil during invasive growth. Recent reports have revealed discrepant PT behaviors between in vivo and flat, two- dimensional in vitro cultures. Here, we established the Stigma- style- transmitting tract (TT) Physical microenvironment Assay (SPA) to recapitulate pressure changes in the pistil. This biomimetic assay has enabled us to swiftly identify highly redundant genes, GEF8/9/11/12/13, as new regulators for maintaining PTs integrity during style -to -TT emergence. In contrast to normal growth on solid medium, SPA successfully phenocopied gef8/9/11/12/13 PT in vivo growth- arrest deficiency. Our results suggest the existence of distinct signaling pathways regulating in vivo and in vitro PT integrity maintenance, underscoring the necessity of faithfully mimicking the physical microenvironment for studying plant cell biology.
Keyword ：
GEF GEF mechano- sensing mechano- sensing microfluidic assay microfluidic assay plant reproduction plant reproduction pollen tube pollen tube
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| GB/T 7714 | Zhou, Xiang , Han, Wenbo , Dai, Jiawei et al. SPA, a Stigma- style- transmitting tract Physical microenvironment Assay for investigating mechano- signaling in pollen tubes [J]. | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 2023 , 120 (49) . |
| MLA | Zhou, Xiang et al. "SPA, a Stigma- style- transmitting tract Physical microenvironment Assay for investigating mechano- signaling in pollen tubes" . | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 120 . 49 (2023) . |
| APA | Zhou, Xiang , Han, Wenbo , Dai, Jiawei , Liu, Sujuan , Gao, Shiyuan , Guo, Yi et al. SPA, a Stigma- style- transmitting tract Physical microenvironment Assay for investigating mechano- signaling in pollen tubes . | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 2023 , 120 (49) . |
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